War of the Huntress
by Mole of Aiur
Summary: Samus Aran, famed bounty hunter, stumbles across a huge discovery. Outside the boundaries of safe Federation space, does she have a chance against this latest threat?
1. No Rest for the Wicked

_Hey guys, I got a bit of inspiration, and so I have begun a Metroid based fanfic. I love the series, and the games are pretty much always near the top of my favourite games list. _

_As for the fic, I hold no rights to anything originally found in games of the Metroid series. All Nintendo's. I have created characters, and they are mine, but that's it. Also, I am aware of the little timeline jitter, but I wanted the old ship with the new AI. Normally in the series that's a Fusion thing. Other than that, I think I'm following the timeline as if Super Metroid had just happened. I'm also using the term cycles for years. Millicycles for the case of this fic are days, centicycles as weeks, and decicycles as months.  
One more thing. My timeline follows that of Wikipedia's, but Metroid Fusion hasn't happened yet. I'm also assuming for the sake of the series wrapping itself up that after the end of the upcoming Metroid Prime 3, Ridley is reverted back to his mostly biological state, as he was in Super Metroid, to help confirm all the timeline problems. Anyway, enough of my jabbering. Read on, and I hope you enjoy my first chapter… Reviews are welcomed!_

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Chapter 1: No Rest for the Wicked

"Must you insist on blowing things up on almost every mission, Samus?" questioned the sentient program running the computer of the gunship of Samus Aran, intergalactic bounty hunter, liberator of worlds. She had just fled from the surface of the rebuilt Planet Zebes, before the planet self-destructed to atoms. She had just single-handedly took down the four guardians of New Zebes, including two of the Space Pirate commanders, Kraid and their leader, Ridley, before destroying the Mother Brain, with help from a Metroid hatchling she had retrieved from planet SR388 cycles previously. Unfortunately, that was the last known Metroid, and it had given up its life to save Samus.

"Lady, you were also supposed to retrieve the hatchling back from Ridley, before it could be cloned for use by the Space Pirates. Where is the hatchling?" Asked Adam.

"I don't cause half of the explosions, Adam!" she argued back, frowning as she removed her helmet, her hair falling out at the back and sides. Her pale face was stained with tears; She knew what the last Metroid had done for her, and yet she couldn't save it.

"-And I know full well what I was supposed to do, you stuck up program... Mother Brain killed it." she added, wiping her face quickly before she turned to face the cockpit of her ship.

"Oh come now, was it not you who destroyed Metroid Prime on Tallon IV, causing the Artifact Temple of the Chozo to cave in after exploding?" it pointed out to the Chozo-infused human survivor of the K2-L raid, fifteen years previous.

"That's not fair! How could I have prevented that?" she exclaimed, glaring at her ship's main touch screen.

"Point taken, Samus. Then how about the entire destruction of Zebes, not once, but now TWICE?"

"I didn't set those bombs!" she snapped, sitting at the cockpit. "Plus, all of these were for the best anyway…"

"I know, Samus. It was my best attempt to be "kidding", as best a program could do so. Remember, I've seen all of your exploits through your HUD." the computer explained. "I apologize, Samus. I saw exactly what happened in the tunnels of Zebes, and I know that you couldn't do anything to help it. You mustn't feel too bad. It was the hatchling's choice. It seemed like it thought of you as its mother figure, so it protected you with its life."

"There's a reason computers can't joke, Adam…" she retorted, sniffing once and crossing her suited arms over her chest.

The ship sped around a large asteroid, as Samus donned her helmet again, before inputting a code into her Arm Cannon. All of a sudden, her Varia Suit glowed, before disappearing, leaving her in a training suit and with her customised GF pistol.

"That's a bit better… You have no idea how heavy that thing is." she said to her computer, who she had named Adam, after her previous Commanding Officer, before he was killed in a skirmish with a Space Pirate Frigate.

"98.5 pounds, Samus. You forget again that I can easily read the dimensions of anything within the range of my optical scanners. In comparison, your Chozo infusion has helped you to cope with the weight. Furthermore, the suit is incredibly light for everything that it consists of, thanks to the technology of the Chozo. It was a good job that you did not destroy Aether, as the Luminoth seem to have a similar level of technology and intelligence to your fostering race. Pity that our visit to such a planet was so short, I would have found it interesting to analyse their race."

"Yeah… You try saying that about my suit if you explored an entire planet in it within a day. Anyway, where exactly are you taking us? I only ordered you to leave Aether's orbit." she asked Adam.

"I assumed that you would require rest, so I am taking you to the closest Galactic Federation frigate. It is currently 1.4 hours away. True, it is even closer to the border GF governed space than Aether was, but it is our closest choice, with the next closest being 3 millicycles away."

"Er… Good thinking, then." Samus said, sheepishly, as she noticed the coordinates planned on the nav-console as Adam had explained. "…Oh."

"It is because of its position that I advise you to put your Suit back on for the time being, Samus. I'll prepare the recharge port now." said Adam, and a whirring sound coming from the right of the cockpit signalled that the Arm Cannon jack had appeared from the wall, ready for use.

"Considering you were designed by the Federation, do you have any real idea what is actually outside of GF boundaries?" she asked, punching another code into the side of her pistol, and in an instant, her Varia Suit materialised around her.

_Booting up primary survival systems… COMPLETE_

_Booting up shields… COMPLETE_

_Loading weapon systems…  
-Power Beam… ACTIVE_

_-Wave Beam… ACTIVE_

_-Ice Beam… ACTIVE_

_-Spazer… DEACTIVATED_

_-Plasma Beam… ACTIVE_

_Loading Morph Ball technology… COMPLETE_

_Loading Boots and Miscellaneous expansions… COMPLETE_

_Suit loaded. Good evening, Samus. _

Samus positioned her Arm Cannon into the wall jack, and felt a rush of energy once again.

_Recharge complete._

"Umm... Samus, we may have a problem." said Adam. Samus rushed to her seat and looked out.

"What is it, Adam? I can't see anything."

"That's the problem. The frigate was last known to be at these coordinates…"

"Pirates?" asked Samus, knowing the answer already.

"Quite possibly."

"How come we never got a distress signal?" Samus asked infuriated, slamming her armour-clad fist into an empty panel in front of her.

"You are forgetting that this is on the very boundaries of GF space. The signal may have been interrupted, and if received, too faint to decipher."

"I wouldn't have thought those bastards could be so tactical without a leader. Ridley's in a million pieces back where Zebes was-"

"Well, All of the events back on Aether were performed without the command of Ridley, Kraid or Mother Brain, to the best of our knowledge anyway." Adam explained.

"Are you saying there is any chance that any of those are alive? I just blew the damn planet up-"

"-Sorry to interrupt you Samus, but sensors are reading huge levels of Space Pirate activity in this sector. There is also another reading… A ship of unknown origin, single seater, headed towards us. Cannot confirm threat level."

"Who the hell is flying around here in unmarked space?" Samus exclaimed in surprise, a little cautious.

"Remember that this ship has no armed defences. The ship is approaching fast. Very fast indeed, the speed nearly matching that of this ship, Samus."

Samus checked the radar, blinking with two lights; Samus' ship in the center, the other ship closing in on its position.

"Well, it's not a Pirate cruiser. Those aren't that fast…" she mentioned.

"Incoming transmission from the ship, Samus. Patching through now."

"Samus? Samus-freaking-Aran? Boy are you a sight for sore eyes… What are you doing way out here?" the voice of a gruff man came through the communicator. Samus opened her eyes wide at the voice. She recognised it.

"Weston? Commander Weston?" Samus voiced back.

"GF Sector K Marine Corps, the very same, kid. Good thing you remember me. I didn't want you blasting me out of my ship." Weston answered.

"Well er… I couldn't anyway. This ship has no weaponry."

"…You need a new ship, kid. Especially round here, Pirates everywhere. Surprised I made it so far without being tracked." said Weston.

"Ms. Aran is fine with the ship she has right now, thank you, Commander." said an offended-sounding Adam. Samus rolled her eyes behind the darkness of her tinted visor; Even programs feel pride, it seems. Although, Samus thought, Adam has proven himself to be more than your normal everyday program.

"Anyway, you after the GF frigate around these parts? Give up now, 'cause I was the ranking officer on that pile of nuts and bolts. Once the Pirates heard about a borderline Federation station, it was a slaughter… I recovered a few men and made a run for it in the escape ships, but we were separated in the firefight. Still dunno even now if they're alive or not." Weston explained, a solemn expression plaguing his otherwise handsome face on the fuzzy holograph screen as he remembered the events.

"One more reason for me to hate the Pirates…" Samus muttered to herself more than anyone. She had a score to settle with the Space Pirates. She had already avenged the many lives of the people of K2-L, including her own parents, three times over. The Space Pirates had managed to rebuild their leaderseveral times She had just destroyed him yet again, and hopefully for the last time. Piece by piece, Ridley had lost to Samus' heavy arsenal over the cycles. She wondered if they would ever meet again in the future. She didn't doubt the possibility. Every time Ridley came back, he was much stronger than before.

"He was bad enough on Zebes…" slipped out of her mouth, causing confusion for the sentient and the commander.

"Samus, we have an emergency. We are being scanned, and not by Commander Weston. Retrieving course now… A planet not far from this position, 4.5 trillion teratons in size. Checking Federation references… Inconclusive. This planet is unknown to the Galactic Federation, Samus." Adam interrupted Samus' thoughts.

"Do I have to explore another planet this decicycle…?" Samus complained.

"Samus, I have calculated the signal frequency of the scanners. They match that of the Space Pirates!" Adam added.

"What?! How did they-" Weston began, but was cut off by the bounty huntress.

"Dear Chozo Gods, we've found the Pirate homeworld…"

"Rather, it found us, Samus…" Adam interjected.

Samus didn't know whether to feel fear or exhilaration. She had finally found the mainstay of the Space Pirates, albeit under unfortunate circumstances. There was a chance at vengeance, at last. But they already had the advantage. A glint appeared in her eyes, and then a broad smile crossed her lips.

"Adam, try and get us on that planet. I have a fight to finish." she said, cocking her Arm Cannon onto her shoulder.

"Samus, you do know that if we land, there is a high possibility that a new mission will have to be made. As your CO, I would have to assign you for once to destroy this planet willingly, wiping the planet clean of Space Pirate activity on the way. Any objections, Lady?"

"None at all, Adam. None at all." Samus answered, an uncontrollable grin spread across her face behind her visor.

"Samus are you NUTS?" The holograph of Weston yelled at her. "Look, I know you're good. I've heard what you've done and I believe them, but this is way too much even for you! We'd need a full scale GF fleet to take on the base of these bastards! You're one woman!"

"Correction, my dear Commander, we are one man, one computer, and one woman."

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_So, Samus has found the home planet of the Space Pirates, or rather, the other way round. What chance could the Huntress have? Then again, she's surprised us in the past.  
_

_Chapter 2, coming soon!_


	2. Roles Reversed?

_Hey everyone, Chapter 2 is finally up. But first, I have a few reviews and queries to try and answer:_

_alleycat1312- I hope I answered your questions through the PM I sent you. I hope that sorted a few things out.  
Mr. Anon- 1) In this, I'm putting it through that somewhere in this timeline that Samus may have had a slip of the tongue and actually called him Adam once, and it stuck. 2) Samus isn't totally GF property, is she? She was raised by Chozo, and has been around the Pirates so long that the whole "cycle" system may have rubbed off on her. I believe that I was a wrong choice in words when you said "Metric" anyway, unless I'm mistaken and am answering another totally different point altogether. If so, sorry. ;;  
_

_Anywho, review, er… reviews are done, on to Chapter 2. Hope you enjoy and give me lots of lovely reviews to read._

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**Chapter 2: Roles Reversed?**

"Oh hell no, Samus. You're not dragging me in on this suicide mission!" Weston exclaimed at the idea of landing on the planet with Samus, against countless Space Pirates.

"Fine, hover around in uncharted space, running away from all the Space Pirate scans, which will no doubt be filling this sector after me." Samus sighed. She started inputting commands into the ship's nav-com.

Weston looked anxious. He looked like he was tossing the situation over in his head, and it looked like it hurt. Finally, he sighed, giving in.

"Alright Samus, you win. Adam, send me the coordinates too. I mean, we can't be sure that it's the Pirate base yet, right? There's a possibility we've been jumping to conclusions here?" Weston said pleadingly, hoping for someone or something to agree with him. He looked closer at his side of the screen. "Is she always like this?" he asked, directed at Adam.

"Actually, I've noted abnormalities in Samus' heart rate and metabolism. The readings are much higher than normal, bringing me to a conclusion that Samus is… excited. She has always seemed so serious in missions in the past..." Adam replied, in a curious tone of voice.

Samus buckled in, and the ship sped off, quickly followed by Weston's ship. It followed the same kind of design, except it was a brilliant silver colour, and it didn't have the technical customisations that Samus had added to her own gunship over the cycles. Most notably, his ship didn't have a resident AI, due to the Commander's stubborn nature when the plans were discussed with him. He had said that he preferred to "wing it" most of the time.

As they approached the planet which the signals had come from, the planet growing larger all the time in the ships screens, Adam contacted Samus, and Weston through a comlink.

"Prepare for landing. Atmospheric scans show that the air is composed of 25 oxygen, 5 nitrogen, 68 sulphur, 2 trace elements. Protective suits and helmets must be worn at all times. Air is unbreathable, and quite toxic."

The ships entered the atmosphere of the huge planet through a small electrical storm, but Samus and Weston had explored way too many planets to be caught out by a storm. Both ships were totally insulated and protected, until they touched down on the surface.

Samus' gunship hovered three feet from the surface, and Weston's ship sprouted six insect-like stands, which planted firmly into the ground. Weston left the sanctity of his ship, walking out by a movie-style fold-up walkway, Samus landing on one knee right in front of him.

"You always have to do that?" he asked, smirking.

"Sorry… Kind of a habit nowadays." Samus replied sheepishly, getting to her feet and looking around. She powered up her Arm Cannon, while Weston prepared his plasma rounds in his customised GF-24K tactical rifle. It carried a lot more ammo, and kicked out extreme power, compared to the standard Federation ones. Samus whistled in admiration as he cocked it over his shoulder.

"You know it." he laughed.

As Samus scanned around with her visor, she started to get interference when facing north.

"Adam, what is this? It's gone fuzzy!" Samus complained.

"Simply magnetic interference, Samus. It seems we have landed quite close to the northern pole of the planet. The fact that it is greater than any other planet we have explored however, makes me curious as to the composition of the planet itself-"

"_Later_, Adam…" Samus sighed. "I can tell this rock's a weird one already… Right Weston?"

"No doubt about it babe. I'm getting freaked out just looking around." Weston replied.

"Don't. Call. Me. _Babe._" strained Samus, who sounded like she was gritting her teeth. She had gained a grip on her Arm Cannon, starting to raise it up to Weston.

"Whoa, okay, okay… Jeez… Sorry Samus." he said quickly, to which Samus lowered her weapon.

"No wonder I work alone…"

"Samus! I've intercepted a message! I'll send it through your helmet…" Adam sounded, alarmed.

And for good reason too. What Samus saw next was what looked like a command center, with two Space Pirates behind the seats, glaring at the screen. Samus jumped, startled, before regaining her composure. Her eyes opened wider when she noticed other Pirates in the background, fighting with masses of Metroids, along with tens of broken, opened stasis cells. One of the Pirates at the front desk raised a clawed hand to the screen, and started making a rasping sound, similar to that of a crocodile, along with many other different reptilian sounds. Adam quickly uploaded a Space Pirate translator, and it revealed what the Pirates were saying.

"_The Hunter has landed, but this time she is not alone. Approach with the full force of the Space Pirate legacy! Eliminate the one threat to those against the Galactic Federation! Do not stop until the Hunter and her new friend have been destroyed! Crimson section, out."_

With that, the connection to whoever the important looking Space Pirate must have had ended, but Samus was still left staring into the furious eyes of the Pirates, as a smaller one arrived the command desk.

"_Crimson Leader, preparations are complete for the Hunter. Repairs have been completed. He is ready, sir."_

"_Samus Aran will not even make it here, let alone to him. But good speed nonetheless. Commend your Cadre, Squad Leader." _the Leader said. The two Pirates raised their arms diagonally upwards across their torsos, their elbows at the hip, and their haunting clawed hand near their opposite shoulder.

The transmission ended, and Samus was left with the view of her surroundings once again.

"The Pirate salute of honour. Pff… Like Pirates actually have any honour." Samus commented over to Weston, looking at Samus bewildered. He hadn't received the feed.

"So er… What did you see, Samus? What does it mean?" Weston asked anxiously.

"Well, we now know that this is the Pirate base. Someone important has been revived for the Pirates, but they didn't say who. Pirate squads are hunting us down, and this all means that we are in serious sh-"

"Samus, I'm reading many bio signs closing in on this position. The Pirates have already mobilised." Adam interrupted, leaving Weston looking mortified. He and Samus quickly looked around, trying to work out the reptilian, yet bird-like shapes of the Space Pirates.

"Samus, I hope whatever luck you live by holds out for us too. Adam almost sounded worried." Weston said, unable to hide an uneasy shake in his own voice. Samus looked at him and frowned.

"Exactly how many solo missions have you been on before this one?" she asked curiously, paying more attention to the surroundings though, moving her Arm Cannon across her field of vision.

"Well, I, er… Being a Commander, I usually have a whole bunch of troopers with me when I go on missions… I'm not inexperienced, I hope you know that Samus, but being on my own and especially on this planet gives me the jeebies…" explained Weston, hopping to turn in place when he heard some stones start rolling to his left, catching Samus' attention too.

"Funny, I can't see anything. Must've just been the wind. Unless… First attacks are usually stealthy…" She muttered to herself, switching her visor to an overall thermal view, and immediately she spotted around five Space Pirate shaped blobs of heat, creeping toward the two hunters. "Weston, look out, they're using cloaking! I've dealt with these kind of Pirates before, don't worry. They can't hide from m-" Samus began, but stopped abruptly when the heat signatures disappeared from her thermal view. "…What?"

Adam monitored this back in Samus' ship console, already noticing differences in build and hunting movements compared to the Shadow Pirates Samus had fought in her previous adventure on Tallon IV. Those Space Pirates used cloaking and charged directly at Samus, before slashing with their attached arm blades.

The Space Pirates that were around Samus now had found a way to hide their heat signatures, most likely by using advanced cooling systems. Moreover, they were using advanced stealth techniques, involving creeping to the enemy and not just charging in.

"Hmm… Interesting indeed…" said Adam, aware that Samus who could hear this would be naturally curious. He continued with an explanation.

"Samus, these are elite class Space Pirates. They are excellent tacticians, and one must be wary. Also, be aware that they may use forms of attack that have been effective throughout the ages, such as-"

"-Flanking! They're probably to our sides as well. Thanks for the help Adam." Samus thought for a moment, before aiming her Arm Cannon directly to her right and fired a blind shot with a Missile. Closer than expected, the Missile exploded, and a familiar snarl of pain sounded from thin air. There was a dull thud, and seconds later the cloaking peeled away of a Space Pirate as it died clinging to a shield of some sort. Samus quickly scanned the shield and allowed Adam and the ship's computers to quickly analyse it, leaving Weston staring at what just happened in disbelief.

"Now, you are either very lucky, or you're damn good!" he said to Samus, smirking.

"I like to think I'm a mixture of both, Commander." she curtly replied.

"Samus, they're using a new form of technology that emanates from these shields of theirs. From the shields, a field of temperature envelops the user, effectively hiding their heat signatures and giving it even thermal cloaking abilities." Adam reported in to Samus' helmet.

"I'm continually being surprised with these Pirates.. You think you know what they're gonna do next, then the clever little bastards make something new to try and stop it." Samus said aloud while thinking. She remembered all that had just happened; the shield technology, thermal cloaking, and before all that, Weston hearing…

"That's it! They can cut off the heat they make, but they still make a damn noise! You're a genius, Weston!" Samus exclaimed, finally working out a way to combat this new threat. She pushed another command into her Arm Cannon, before her visor went mostly black, leaving behind ghostly white figures of creeping Space Pirates, and an overall faint grey view of her surroundings.

"Ah, the Echo capabilities Samus? Good thinking…" Adam commented, surprised at Samus' intuitiveness. "This may even the odds."

"May? Adam, how long have you worked with me?" Samus said, grinning to herself, as she started aiming at the Space Pirates, looking over to the perplexed Federation commander for a moment.

"Weston, either spray with that gun of yours or get somewhere safe. I can handle these now."

"Oh come on Samus. You think I'm the type to run and hide?" Weston sneered, cocking his rifle and putting it to his face to begin aiming. "I landed with ya, I'm fighting with ya. Got it?"

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_Alright then! Sorry for the wait, I had a little bit of block, and I was a tad busy. Chapter 2 is complete, and the two hunters have to get in gear pretty quickly if they're to survive on this planet. Reviews welcomed._


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